These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Cult Classic: Considered by fans to be a forgotten Disney classic.
Ensemble Darkhorse: Captain Amelia, partially due to being the major Token Chick in the film, considering that there was a severe lack of female characters in the original Robert Louis Stevenson novel, mostly because she's a Badass, snarky, Lady of War.
Fanon: Fanfic writers have given Captain Amelia the surname Smollett after the captain from the original story.
It Was His Sled: It's Treasure Island—a story that most everybody knows by heart, regardless of whether they've actually read the book. That said, the film does add it's own twists and unique ideas of it's own here and there, but don't expect any major surprises.
He is also shipped a lot with Silver, and on the crossover slashy side, Sinbad, Aladdin or Dimitri are popularly shipped with him. Let's just say for a film featuring one of Disney's (Renaissance-onward) rare celibate heroes, the fans really like the idea of him find more adventures out there...
Moral Event Horizon: We get the idea that Scroop is a nasty guy, but then he proves it even more by gleefully sending Mr. Arrow to his death via black hole (ironically, black holes are the trope namer) only to turn around and place the blame entirely on Jim. In the end, Jim sends him tumbling into space in a similar manner.
Scroop: "Do say hello to Mr. Arrow for me."
Jim: "Tell him yourself!"
Nightmare Fuel: As soon as you see Scroop with the rest of the crew, you just KNOW he's the one you really do not want to be alone with.
While we're on the subject of Scroop, on the ship when Jim steps out to shoot at Scroop, the lights suddenly go out, courtesy of B.E.N., who is trying to disable the laser cannons, and the emergency lights turn on, revealing Scroop has disappeared. As Jim looks around, Scroop appears above him about to strike.
In a subtler way, the revelation that Silver is planning treachery (along with either murder or a mass marooning) makes his pleasant behavior quite chilling.
The confrontation between Jim and Silver after Jim overhears the mutiny. As they're both speaking, Silver turns his mechanical arm into a pistol behind his back, obviously intending to shoot Jim.
No Problem With Licensed Games: The PC RTS, Battle At Procyon, taking place five years after the movie, with a storyline based around Jim raising through the ranks of the Royal Navy.
In addition, the game of the movie was considered pretty good in general.
The film boasts probably the most impressive blend of CGI and hand-drawn animation ever attempted. Highlights include Silver, whose mechanical parts are CGI while his organic ones are drawn, and B.E.N., who is the film's only CGI-only character. Both instances blend almost seamlessly with the hand-drawn material.
The Scrappy: B.E.N. to some people. He almost. Never.Shuts.Up. A Large Ham and a bit of a Butt Monkey. The other characters also find him annoying, but because the other characters are actually sympathetic which can make him even more dislikeable to some.
The Woobie: Jim could easily fall into woobie status, given his Disappeared Dad, stressful home life, and the unbelievable amount of abuse he receives from pretty much every character except Delbert and B.E.N.